Microbio After Midterm Flashcards

What are key principles in specimen collection?

-Verify you are collecting from the correct patient

-Ensure you have the correct equipment (collection container, swabs, expiry date, labels)

-Collect from site of infection

-Avoid contamination from normal flora and maximize ability to isolate pathogen

-Correct timing (early in day for TB, prior to antibiotics)

-Ensure adequate volume of sample

-Use appropriate PPE

-Ensure lids are tight to prevent leakage and wipe off blood on outer surfaces

-Use single use items whenever possible

-Use safety engineered needles or needle less systems

-Dispose of sharps appropriately

What are key principles in specimen transportation?

-Package sample appropriately into plastic bags with paper requisition form

-Transport to laboratory ASAP (pneumatic tube system, porters)

-Store in appropriate conditions (room temp or fridge 2-8c to prevent growth)

What are key principles of specimen analysis in the laboratory?

-Ensure appropriate test and specimen for the selected test

-Evaluate if specimen is appropriately collected

-Optimize methods to detect pathogen (direct examination, culture, molecular methods via PCR)

-Determine antibiotic susceptibility

-Report results (EMR, critical calls to MD/RN, IPAC notification)

-Communicate test results of public health significance

What is the preanalytical testing phase for specimen collection?

The phase between examining the patient and sending the specimen to the lab.

This is where most specimen errors occur

What are preanalytical errors?

Errors in specimen collection that occur between first examining the patient and sending the specimen to the lab.

It is where most specimen collection errors occur

What are the consequences of poorly collecting specimens?

-Can affect ability to grow specimen, affecting the quality of reporting requirements and metrics, ability to detect infection, and adequacy of patient treatment

-Requires recollection of the specimen and retesting, leading to decreased patient satisfaction

-Can affect nurses professionalism by decreasing ability to provide proper patient care, increasing exposure to bloodborne pathogens upon collection, and decreasing patient satisfaction

What are two methods in which microbiology tests are ordered?

Via computerized ordering (Epic EMR) or paper requisitions

What is essential information to include on a microbiology test order?

-Unique identifier of the patient

-Gender, Age, DOB (may include different collection protocol)

-Test ordered

-Date and time of collection

-Who requested the test

-Allergies to antibiotics (additional testing may be ordered -> ex: penicillin allergy)

-Specimen type

-Specific anatomic site

-Clinical information (animal bite, travel history, pregnancy, immunocompromised status)

Why is patient identification important during the specimen collection process?

Without correct patient identification, the wrong results can be attributed to the wrong patient

In extreme cases, such as for blood transfusions, it can lead to patient mortality

How must patient identification be confirmed during specimen collection?

Must confirm patient's identification before performing specimen collection (along with any intervention) using two unique patient identifiers (full name, OHIP number, assigned ID number, telephone number, DOB, RFID)

What are examples of unique patient identifiers?

-Full name

-Assigned ID number - OHIP/Medical record number

-Telephone number

-DOB

-RFID

When should you label a specimen container?

At the bedside RIGHT AFTER collecting the specimen from the patient.

The label itself should contain two patient identifiers

When might you prelabel a specimen container prior to collection?

In cases of patient collection (ex: urine culture), must verify patient and label the container in the presence of the patient. If no urine is collected, the specimen should be discarded

What are common errors in specimen labelling?

No label on specimen at all

Specimen is labelled incorrectly (wrong patient + wrong tube contents)

Label is illegible

Label covers up the specimen, meaning that the lab cannot assess the quality of the specimen

Label is applied sideways, which cannot be read by the labs barcode reader

What is the importance of selecting the correct container medium during specimen collection?

Transport media is designed to preserve the pathogen before it is delivered to the laboratory. Some transport media, such as blood culture bottles, contain resins that attach to antibiotics

Which type of specimens should be stored at room temperature?

-anerobic organisms

-blood culture bottles

-spinal fluids for bacterial culture

Prevents overgrowth of organisms

Which type of specimens should be refrigerated?

-Urine

-Sputum

-Bronchoscopy

-Respiratory virus swabs

Prevents overgrowth of organisms

When should specimens be transported to the laboratory?

ASAP

All specimens should ideally be transported within 2 hours

CSF and STAT specimens should be transported within 1 hour

GAS throat swabs, cervical and urethral cultures for N. gonorrhea, Neisseria meeningitidis (CSF + blood cultures, and anerobes will be significantly impcated if there is a large delay in specimen transport

Viruses may be stored for longer periods of time (2-3 days refrigerated) without being impacted

What are the consequences of getting a specimen sample rejected by the microbio lab?

-Delay in diagnosis and correct treatment

-Increased patient discomfort and dissatisfaction from repeated testing

-Increased nursing and laboratory workload

What is the purpose of blood cultures?

Determining if bacteria is present in the blood (bacteremia), which can be caused secondary to a lung, urine, CNS, or soft tissue infection, or primary from a cardiovascular infection (endocarditis, mycotic aneurysm, vascular graft)

When should blood cultures ideally be collected?

Prior to antibiotic administration

How should blood cultures be drawn?

Usually 2 sets consisting of 2 bottles each (4 bottles in total)

Each set should be from a different venous puncture site.

1 bottle per set is for anerobic bacterial growth

the other bottle is for aerobic bacterial growth

At least one specimen set should be collected peripherally compared to drawn from a line as there may be contamination in the lines themselves

How much volume of blood should be collected for blood cultures?

8-10 milliliters for adults, weight based for pediatrics

Why should 2 sets of blood cultures (4 bottles in total) be collected from the patient?

-Higher volumes increase the ability to grow the pathogen and increases the sensitivity of the blood culture

-It is easier to determine contaminants of a sample if 2 sets are available (comparing the two)

Is the timing of the blood culture collection important?

No, the most important factor is the volume of blood collected from the patient

(10ml from 2-3 sets of 2 bottles)

What is contamination of a blood culture?

Presence of normal flora in the culture - causing a false positive culture

Can be caused by improper collection procedure (not keeping sterility) or not collecting enough blood (only collecting 1 set)

What are common bacterial contaminants of blood cultures?

Skin flora

-Coag neg Staphylococci

-Viridans Streptococcus

-Micrococcus

-Cutibacterium

-Corynebacterium

Environment

-Bacillus species

What are methods of decreasing blood culture contamination?

Skin disinfection

-Choosing right disinfectant based on procedure (chlorhexidine, tincture of iodine)

-Ensure adequate contact time of the disinfectant on the skin (chlorhexidine + tincture of iodine ~30sec)

-Allow disinfectant to dry

-Palpate puncture site PRIOR to disinfection

Blood culture bottle preparation

-Disinfect the septum of the bottle

-Avoid placing specimen on non-sterile surface

-Performing hand hygiene

What are the consequences of contaminating blood cultures?

FALSE POSITIVE

-Unnecessary utilization of lab resources

-Increased hospitalization length

-Cost impact

-Unnecessary antimicrobial usage

-Unnecessary additional patient care measures (diagnostic studies, imaging procedures, medications)

When should blood cultures be drawn from lines?

Should only be collected from PICC or central line catheter is a line-related infection is suspected or if the patient is a very difficult draw

At least one of the sets should be a peripheral draw

How are blood cultures analyzed in the lab?

Incubation

-Placed in instrument which incubates the blood culture at 35c to promote bacterial growth

-Presence of CO2 or decrease in O2 is detected by the machine, which signals bacterial growth

-As soon as growth is detected, the machine sounds an alarm, which notifies lab tech to analyze specimen

Gram staining

-Blood cultures are gram stained with a crystal violet stain that results in the organism being purple

-A decolorizing removes the primary purple stain, and a secondary stain is used to view gram negative bacteria

What is matrix-assisted laser desorption/ionization?

Bacterial colonies are placed in arrays which are then placed in a machine that zaps the colonies with a laser - removing the proteins and creating ions which are used to create a "fingerprint" of the bacteria.

This fingerprint is compared to a database in order to identify the bacteria. Results can come back rapidly within 15-30 minutes

What is susceptibility testing?

Determining which antibiotics a bacteria is susceptible to. Can either be done by a machine or manually by inserting paper disks with the antibiotic and analyzing the zone of growth inhibition

This usually takes some time

When should urine cultures be collected?

Should normally only be collected if the patient is symptomatic of a UTI

(Dysuria, hematuria, urgency, fever, rigors, back pain)

Elderly patients - change in mentation, should consider other possibilities + rehydrate before ordering a urine culture

Cases of asymptomatic patients

Routine pregnancy screening at 16-18 weeks

Invasive urologic procedure where bleeding is expected

What are cases where a urine culture may be collected from asymptomatic patients?

Routine screening for pregnant individuals between 16-18 weeks

Invasive urologic procedure where bleeding is expected

What are non-invasive methods of collecting a urine culture?

Urine collected without surgical procedure

1. Clean-catch midstream specimens (by patient)

2. Indwelling and In and out catheter

3. Illeal conduit

4. Bagged specimens in pediatrics

Invasiveness of procedure used to collect the urine culture should be noted as it may be treated differently by the lab (invasive procedures are more sterile -> generally less bacteria collected)

What are invasive methods of collecting a urine culture?

Urine collected during/using a surgical procedure

1. Cystoscopic

2. Ureteral

3.Percutaneous nephrostomy

4.Suprapubic aspirate

Invasiveness of procedure used to collect the urine culture should be noted as it may be treated differently by the lab (invasive procedures are more sterile -> generally less bacteria collected)

What are patient instructions for collecting a urine culture?

For men, ensuring that they properly clean the glans penis

Instruct patient to void urine into toilet - collecting the urine midstream (not collecting the first part of the void) - which prevents contamination of the sample

This is especially important for collecting a specimen from a male

How should a urine culture be collected from a catheter?

Collect sample from sampling port using aseptic technique

Do not collect directly from the catheter bag

What are urine chromogenic medias?

Growth medias which contain dyes that activate based on the chemical properties of the organism

The color of the dye can be used to quickly diagnose the bacterial specimen

How much of a pathogen is required for a UTI to be suspected?

>10-100x10^6 CFU/L of a pathogen required

When will a microbio lab not report organisms within a urine culture?

If there are 3 or more organisms or if a non-pathogenic organism is isolated, the laboratory will not report the organism due to probably contamination of the sample

How should urine cultures be stored?

Should be refrigerated at 2-8 degrees to prevent overgrowth of pathogens and contaminants

May also be preserved with boric acid

What is the best way to collect enough specimen volume from a soft-tissue infection?

Best method is to aspirate fluid or collect tissue sample

If there is not enough fluid, a swab should be used

What is the procedure for collecting a swab specimen from a wound?

Clean area with sterile water or saline with sponge or gauze to prevent contamination of the sample

Apply swab at the advancing margin (edge) of the wound

What are the advantages of collecting a fluid or tissue sample compared to a swab sample for soft-tissue infections?

Collecting fluid or tissue sample maximizes the collected volume, which increases the sensitivity of detecting pathogens. It can also be used to detect both aerobic and anerobic organisms (whereas swabs can usually only detect aerobic organisms).

It is also less likely to be contaminated by skin normal flora

What are common bacterial with antimicrobial resistance (AMR) and multi drug resistance (MDR)?

-MRSA

-VRE

-ESBL

-CPE (Carbapenemase producing Enterobacterales)

-MDR Pseudomonas aeruginosa

-MDR Acinetobacter baumanii coplex

-Serratia marcescenes

-Candida auris

When is a surveillance swab gathered from a patient?

Based on PHAC and IPAC guidelines for risk factors of AMR and MDRs

-Pt was hospitalized at another hospital within the last 12 months (Rx for MRSA, VRE, CPE)

-Pt was hospitalized at another hospital outside of Canada (Rx for C. auris)

-Pt was exposed to another patient who was a known previous positive

Why is C. auris a critical priority pathogen?

C. auris has high rates of antifungal resistance and mortality rates - with high spikes in cases reported in the United States.

As such, C. auris is a reportable organisms (report to public health) in Ontario, along with 2 other provinces in Canada

How is a stool sample collected from a patient?

Patient BM into plastic collection device that fits into the toilet (such as saran wrap over the toilet or a sterile bedpan)

Patient should avoid laxatives or mixing the sample with urine or water

When will a microbio lab reject a stool sample?

-If the incorrect transportation media is used to send the sample

-If a stool culture was gathered 72 hours after the patient is admitted

-For C. difficle the sample cannot be a formed stool or from a patient who is less than 1 years old (use rectal swab)

How are stool samples analyzed at the microbio lab?

The sample is analyzed used molecular methods, specifically multiplex PCR which is able to detect Salmonella, Shigella, E.coli, shiga toxin, and Yersinia entercolitica very rapidly.

Can be used to detect organisms in low numbers and not very stable

What are advantages and disadvantages of multiplex PCR?

Advantages

-Able to analyze strain rapidly

-Able to detect organisms in low numbers and that are not very stable

-Can detect shiga toxin, which is produced by Enterohemorrhagic E. coli (EHEC)

Disadvantages

-Still need to culture to isolate Salmonella, Shigella, and EHEC to perform genotyping for outbreaks and to perform susceptibility testing

What are sterile fluid samples?

Irretrievable specimens (very hard to recollect specimen) which includes CSF, Pleural fluids, joint aspirate, pericardial fluid, and vitreous fluid

How is a CSF sample collected?

Collected using 4 tubes (order of tube collection is important)

Tube 1 -> Cell count

Tube 2 -> Chemistry (Protein + glucose)

Tube 3 -> Microbiology (need larger volumes if fungal or TB cultures requested)

Tube 4 -> Cell count

CSF samples must be sent to the microbio lab within 1 hour (prevent degradation)

What is a critical call notification?

A life threatening result detecting by the microbio lab which is called to the nurse and/or physician which is involved in the care of the patient at the laboratory

What is the microbio lab's role in a critical call notification?

-Indicates that a laboratory result is a critical result

-Asks for full name of individual taking the result

-Provides the lab result

-Asks the individual taking the result to read it back

What is the nurse's role in a critical call notification?

-Documents that they have taken the critical result

-Must call the most responsible physician or physician on call and provide the result (someone must take the result)

How are CSF specimen samples incubated?

Incubated at 35 degrees to promote bacterial growth.

Different atmospheres may be provided depending on the bacteria

->5% CO2 for Neisseria gonorrhea + meningitides and streptococcus pneumoniae

-> Ambient air for Pseduomonas aeruginosa

What microbio diagnostic procedures are performed for a CSF sample?

Gram staining

Culturing (can be falsely negative)

Molecular detection using PCR (may be positive when culturing provides falsely negative result)

Aspiration or biopsy of skin lesion

What upper respiratory bacterial stain is usually tested for by the microbio lab?

Streptococcus pyogens (GAS) due to risk of rheumatic fever)

What microbio diagnostic procedures are performed for a respiratory specimen?

Culturing (most common)

Molecular methods - PCR (Fast results, but more costly)

What microbio diagnostic procedures are performed for a suspected lower respiratory bacterial infections?

Nasopharyngeal or oral/nasal swab for respiratory PCR

Nasopharyngeal swab for Mycoplasma/Chlamydia OCR

Consider culturing sputum and blood cultures for pneumonia

What are molecular methods of analyzing specimen samples?

Can be used to diagnose bacteria, viruses, parasites, and fungi

Nucleic acid is extracted from the specimen or isolated. The nucleic acid is amplified via PCR, strand displacement, transcription related amplification, etc.

What are advantages of using molecular methods for analyzing specimen samples?

-Increased sensitivity compared to culturing

-Can be used to detect organisms which were delayed when transporting to the lab

-Can be used to detect organisms which cannot be cultured

-Can be used to detect organisms more rapidly than traditional methods

-Sometimes can provide a quantitative result

What are disadvantages of using molecular methods for analyzing specimen samples?

-Contamination can occur in the laboratory (amplifying a very small amount of DNA)

-If a mutation occurs, the assay will not detect the organism (database requires continual updating)

-Susceptibility testing cannot be performed

-Can be extremely sensitive - may pick up colonies and not disease

-Results can remain positive for a long period of time, even if the organism is dead

What diagnostic procedures are performed for suspected TB infection specimens?

-Sputum (best collected in the morning - take 3 different samples on 3 different days)

-Bronchoscopy (uncommon)

-Spinal fluid (uncommon)

-Blood culture

-Tissue/aspiration

-Gastric lavage (collecting sputum swallowed by the infant - must neutralize gastric acid)

What fungal strains are classified as "critical" according to the WHO priority list?

-Cryptococcus neofromans

-Candida auris

-Aspergillus fumigatus

-Candida albicans

What is cryptococcus neoformans/gattii?

Type of fungal strain which can cause a CNS or pulmonary infection - usually in individuals which some sort of immunodeficiency (HIV, organ transplant - antirej meds, diabetes, older age, renal and liver disease, biologic meds, corticosteroid meds, immunocompromised)

What are diagnostic procedures performed to analyze a suspected cryptococcus neofromans/gattii infection?

Direct microscopy (organism appear spherical to oval, small, and with narrow budding)

Detecting cryptococcus antigen - very quick to detect

What diagnostic procedures are performed to analyze a suspected aspergillus infection?

-Tissue pathology

-Fungal direct microscopy and culture (scotch tape to look at microscopic features)

-Galactomannan test (conducted on blood and bronchoscopy specimens)

-Aspergillus PCR done on bronchoscopy specimens

What diagnostic procedures are used to detect a malaria infection?

-Blood by venipuncture or capillary puncture (preferred due to higher sensitivity)

-Travel information + symptoms

-Antigen detection

-Blood smearing + microscopy

-PCR test

What is a serology test?

A type of blood test that is used to diagnose acute or chronic infections or the vaccine/immune status of an individual based on the presence of antibodies (IgM, IgG) or antigens (Hep B sAg for Hep B infection)

What are immunoassays?

Tool used to detect presence of antibodies and antigens from a patient sample

An enzyme immunoassay is the most common method that is used, where an labelled enzyme is used to react with the sample to detect antibodies or antigens

What is bacteremia?

Presence of bacteria in the bloodstream that may or may not cause symptoms

What are three categories of bacteremia?

Transient Bacteremia (No symptoms or disease, self-resolving, usually in patients with a sufficient active immune system or without turbulent cardiac blood flow (resulting in endocardium damage))

Primary Bacteremia (Bacteria directly enters bloodstream, usually caused by healthcare acquired infections - IV)

Secondary Bacteremia (Opportunistic, bacteria disseminates from original site, starts in an organ like lungs)

What is sepsis?

Organ dysfunction caused by body's intense immune reaction to an initial infection. The body's immune system is responsible for the organ damage

What is septic shock?

A category of sepsis that causes circulatory and cellular/metabolic abnormalities which are profound enough to increase mortality

What is endocarditis?

Infection of the endocardium, the innermost layer of the heart that lines the chambers and covers the valves, usually caused by damage to the endocardium, resulting in vegetation (bacterial/fibrin/platelet deposition) and usually impacting the heart valves, resulting in possible heart failure or emboli formation

What is myocarditis?

Infection of the myocardium, the muscle layer of the heart, usually caused by a viral infection, resulting in mild heart failure symptoms. Often co-occurs with pericarditis.

What is pericarditis?

Infection of the pericardium, the outermost layerthat encloses the heart, usually caused by a viral infection and co-occurs with myocarditis. Results in positional pain as the layers of the pericardium rub together.

What causes rheumatic fever?

A complication of streptococcal pyogenes/pharyngitis, where untreated infection causes an autoimmune reaction since the antigens associated with the bacteria species is similar to host tissues, resulting in autoimmune mediated tissue damage that attacks the heart (carditis), attacks the joints (polyarthritis), causes rash (erythema marginatum), and causes motor disturbances (chorea)

What specifically causes the manifestations of rheumatic fever?

Immune response from attacking streptococcal pyogenes causes damage to host tissue as well

What bacteria species causes rheumatic fever?

Streptococcal pharyngitis

What are manifestations of rheumatic fever?

Carditis - Inflammation of the heart, causing acute valvulitiis (inflammation of valves - esp mitral), leading to symptoms of heart failure and progressive heart valve damage (predisposing pt to endocarditis)

Polyarthritis - inflammation of large joints, lasting 2-3 weeks

Erythema marginatum - Rash on trunk

Chorea - Motor disturbances

Symptoms should resolve on their own

What is the treatment of rheumatic fever?

No "cure", requires symptom management until symptoms resolve on own

High dose NSAIDS (ASA) for inflammation

ACE inhibitors and Beta Blockers for heart failure symptoms

Antibiotic therapy to treat streptococcus pyogenes (even if no symptoms of infection, making sure bacteria is completely cleared out)

Valve replacement if residual heart disease (persistent valvular disease) after infection (Percutaneous mitral balloon commissurotomy)

What is residual heart disease from rheumatic fever?

Persistent/chronic valve disease after rheumatic fever, aka rheumatic valve

What are prevention techniques for rheumatic fever?

Providing antibiotic prophylaxis (penicillin) for patients who have had rheumatic fever.

What is the antibiotic prophylaxis protocol for patients who have had rheumatic fever with no residual heart disease?

Penicillin every 4 weeks until...

21 y/o

OR

10 years after last rheumatic fever

What is the antibiotic prophylaxis protocol for patients who have had rheumatic fever with residual heart disease?

Penicillin every 4 weeks until...

40 y/o

OR

10 years after last rheumatic fever

OR

May need lifetime antibiotic prophylaxis

What antibiotics are prescribed for antibiotic prophylaxis for rheumatic fever?

Benzathine penicillin IM

If patient has true allergy, Azithromycin and erythromycin is prescribed

Why are patients with rheumatic valve at a higher risk of getting endocarditis?

Dysregulated valve can cause turbulent blood flow, resulting in endocardium damage.

The damage allows for deposition for fibrin, platelets, and bacteria, which can lead to endocarditis.

This means that even transient bacteremia can become a problem as there is a higher chance of leading to endocarditis

What is transesophageal echocardiogram?

Capturing images of the heart structures by inserting a probe through the esophagus.

This technique is preferred as it reduces shadowing associated with transthoracic echocardiograms due to the ribs

What is vegetation in endocarditis?

Infectious masses growing on the heart valves which is the result of an accumulation of fibrin, platelet, and bacteria from endocardium damage

What are two categories of endocarditis?

Subacute endocarditis (symptoms develop over weeks/months - fatigue, weakness)

Acute endocarditis (symptoms develop rapidly - fever, tachycardia, chills)

What causes endocarditis?

Damage to the endocardium caused by turbulent blood flow (valve damage, prosthetic valve, implanted device, drug use) results in deposition of fibrin, platelets, and bacteria (often from normal flora or transient bacteremia), causing vegetation formation and can lead to thrombotic events (heart attack, stroke, MI, vascular insufficiency)

What can be heard on heart auscultation for patients with endocarditis?

Heart murmur ("hearing" turbulent blood flow over vegetation)

What are clinical manifestations/symptoms of endocarditis?

Peripheral

Splinter hemorrhages

Janeway Lesions

Osler's nodes

Roth spots

Thrombosis

Pulmonary emboli

Myocardial infarction

Stroke

Seizure

Vascular insufficiency - tissue necrosis

Cardiac

Heart failure

Valvular damage

Heart murmurs (on auscultation)

Non-specific

Fever

Tachycardia

Fatigue

Coughing

Chest Pain

Weight loss

What are four peripheral manifestations of endocarditis?

Splinter hemorrhages (lesions in nails)

Janeway lesions (Lesions on hands/feet)

Osler nodes (Painful swelling of fingers and toes)

Roth's spots (Pale hemorrhage in conjunctiva

These symptoms are non specific but are consistent findings with endocarditis patients

What are splinter hemorrhages?

Painless lesions on the long axis of distal third of nail.

Usually red in appearance, and then turns brown/black

Non-specific peripheral manifestation of endocarditis